The Diocese of Madagascar was established by Patriarchal and Synodal decree on September 23, 1997. Prior to the formation of the Diocese of Madagascar, the territory of the diocese was part of the Archdiocese of Zimbabwe. During the Fall 2012 meeting of the Holy Synod of the Church of Alexandria the Diocese of Madagascar was elevated to the Archdiocese of Madagascar.

On February 16, 2008, His Beatitude Theodoros II inaugurated a new seminary near the valley of Alasora in Madagascar that was financed by the faithful in Australia, adding a new institution to those seminaries in Alexandria, Nairobi, and Kinshasa.